The complete genomic sequence of normal human apoC-II has been elucidated from an apoC-II clone isolated from a human placental genomic DNA phage library. The normal apoC-II gene consists of 3407 base pairs and like the genomic structure of other known apolipoprotein genes it contains 3 introns and 4 exons. DNA isolated from the WBC of 6 different patients with apoC-II deficiency was isolated and analyzed by Southern blotting using an apoC-II cDNA probe. The restriction endonuclease digestion pattern in 5 patients were normal but Southern blot analysis of one patient showed a major rearrangement in one of the apoC-II alleles suggesting there is a large insertion of deletion present. The apoC-II gene from two of our patients with apoC-II deficiency has been cloned into an EMBL-3 lamada vector genomic library. Several apoC-II clones have been isolated from each library and determination of the complete genomic structure of the potentially defective apoC-II gene is underway to determine the specific molecular defect. Total RNA from the liver of one of the patients with apoC-II deficiency has been isolated. Northern blot analysis reveals a normal size apoC-II mRNA and quantitation by slot blot analysis shows near normal levels of apoC-II mRNA in this patient suggesting the possibility of a post-translational defect.